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Running a galaxy workflow

In this use case, we are going to

  • Upload a workflow description files in your Galaxy server instance
  • Visualise this workflow and its tools
  • Eventually run the workflow on input data obtained from a remote public repository.

1. Upload workflow description file (.ga)

  • Click the workflow menu
  • Click the "Upload or import workflow" button at the top right

  • In the Galaxy workflow URL: field, paste the url of the workflow file: 

    https://raw.githubusercontent.com/ARTbio/AnalyseGenome/main/Exercises/Galaxy-Workflow-Extract_canonical_transposons_fasta.ga
    Note that this file is in the artbio/AnalyseGenome repository where material for this training is hosted

  • Click on the Import button

Note

Alternatively, you could upload the workflow files from you computer instead of uploading them by URL

  • the Workflow menu should now look like :

imported workflow

  • Click the workflow Extract canonical transposons fasta (imported from URL) and the Edit option

clean workflow

We can go through the various steps of the workflows and figure out what they are doing.

This workflow performs a series of find-and-replace text manipulations, starting from input data that has been tagged transposon_set_embl.txt and producing a new text dataset that is renamed Canonical_transposons.fa.

4. Retrieve the transposon_set_embl.txt dataset

  • Create a new history and name it workflow test

  • import the dataset

    • Either using the Paste/Fetch data mode of the upload manager (the small bottom-top arrow icon at the top left of the Galaxy interface). Copy the URL 
      https://raw.githubusercontent.com/bergmanlab/drosophila-transposons/master/releases/transposon_sequence_set_v9.5.embl.txt
      in the open field and click the Start button.

    • OR, remembering that you just did that few minutes ago !

      Thus, you can use the copy datasets function which allow to copy datasets from history to history !

      How to copy a dataset from an existing Galaxy history
      • Click the wheel icon at the top of your history right bar

      - Select EMBL to Fasta conversion in the Source History left panel - Check the item 1in the list (should be transposon_sequence_set_v9.5.embl.txt) - Verify that the history in the Destination History right panel is workflow test (should be by default, otherwise change it) - Click the Copy History Items button - Observe the dataset showing up in your test workflow history !

  • have a close look at the dataset

5. Run the workflow

  • Click on the workflow menu
  • Click the Run option of the workflow (the ▶ to the right hand side)
  • Select the appropriate dataset (should be only one already selected)
  • And Click the Run workflow
  • Look at datasets in the history turning from grey to yellow to green and eventually getting hidden.

6. Check result

You may check that the generated dataset is identical to the one generated with the tool embl2fa using the tool differences between two files

7. Goody for you: an exemple of workflow to treat complex data table

As this is a goody, we put here the key steps to run the workflow

  • Workflow URL 
    https://raw.githubusercontent.com/ARTbio/AnalyseGenome/main/Exercises/Galaxy-Workflow-process_diffmod_table.ga
  • 2 tools must be installed in your Galaxy instance to get the workflow running:
  • add_column_headers
  • column_maker
  • Input table to be parsed/transformed 
    https://github.com/ARTbio/AnalyseGenome/raw/main/Exercises/diffmod_table.tsv.zip